Biochar has been exploited as a substitution of carbon black in the rubber industry and various biochars exhibit diverse reinforcing abilities due to the different compositions. This work aims at studying the effect of silica on the modification process and reinforcing performance through the comparison of three biochars with different contents of silica, pyrolytic rice husks (PRH, 34 wt%), pyrolytic bamboos (PB, 7 wt%) and pyrolytic corn cobs (PC, 0.4 wt%). The results reveal that PRH requires higher rotational speed (300 min–1) than PB (200 min–1) and PC (200 min–1) to achieve similar particle sizes during the ball milling process because of the aggregations of higher silica content. Meanwhile, silica-rich pyrolytic biomass exhibits enhanced reinforcement on mechanical properties and thermal stability of rubber, and the elongation at break of vulcanizates continues to improve with increasing silica contents. Combined with the energy consumption and reinforcement, biochar containing a little amount of silica is more suitable to be widely used as bio-filler in rubber industry. This work should serve as a valuable reference to select appropriate biochar for the production of bio-fillers with high reinforcement.